Scattered across East Anglia are around 400 medieval painted rood screens that survived the desecration of the Reformation and the civil war. But now they are under threat of a different kind of destruction.

These extraordinary masterpieces – the largest concentration in northern Europe – are tucked away in tiny, often remote parish churches, and many are virtually unknown. The biblical and historical figures painted on oak panels in the 15th and early 16th centuries include saints, apostles and kings.

Although some are still in good condition, experts say many are slowly and irreversibly deteriorating, partly because of a lack of funding. They say at least half are in serious condition with flaking paint and splitting wood.

Fluctuating temperatures and humidity levels, partly due to heating systems to keep worshippers warm, are taking their toll, encouraging insects that eat the wood.

The problem is exacerbated by the struggle of parishes to keep churches weather-tight with shrinking congregations to help fundraising. The cost of replacing a leaking roof alone can exceed £100,000.

Tobit Curteis, a leading architectural conservator, said: "These are fantastic medieval panel paintings. In a gallery they would be vastly famous but dotted around churches they're largely unknown, except amongst specialists. The screens are among the few insights that we have into the richness and colour of the pre-Reformation church."

But he warned that owing to their vulnerability, without action "these wonderful treasures will slowly disappear. In most cases it won't be sudden, but our grandchildren won't see them. A tragedy!"

Curteis is involved in a pilot project organised in conjunction with the Church of England and the Hamilton Kerr Institute, University of Cambridge, to create a conservation plan. It has received £40,000 from the Headley Trust, but that is a fraction of what is needed for the main project.

Rood screens – "rood" was the Old English word for cross or crucifix – are enormous, some three or four metres high. Designed as a spiritual barrier separating nave from choir or chancel, the public part of the church from that of the priest, the crosses in East Anglia were systematically removed in the Reformation.

Screens are suffering fungal attack and damage from bat faeces, and roughly one in five of those surveyed showed signs of death watch beetle. Lucy Wrapson, of the Hamilton Kerr Institute, said: "There are a lot of problems with damp and raised paint, flaking … You've got scattered white losses over the surfaces of these paintings."

She said that more extreme weather as a result of climate change was likely to make buildings less able to cope. "I don't think the current model for their maintenance is either working or sustainable in the long term."

She echoed Curteis's view that unless an artwork was in a museum it was not thought valuable. She said: "Many are of museum quality. But they don't tend to get elevated in the same way."

She was shocked to discover paving slabs and a spade leaning on medieval paint on a screen in one church in Norfolk. In another, a sequence of saints on a screen in the vestry had such a darkened varnish that many people did not realise they were painted. "Chairs and tables are stacked against them," Wrapson said.

The East Anglian painted screens are the largest surviving collection of medieval painting. The jewels include 15th-century screens at the Church of St Michael and All Angels, in Barton Turf, Norfolk.

Rupert Featherstone, director of the Hamilton Kerr Institute, spoke of his alarm at paintings "in a very poor state". Of the entire collection of painted rood screens, he said: "There's nothing similar in Europe. They're important to the world."

Janet Gough, director of cathedrals and church buildings for the Church of England, said: "Parish churches have huge demands on their resources. Of course, the conservation of art objects comes low down on their list of priorities … But this is our national heritage. It's not just about often hard-pressed church communities."